[FieldTrip] Coherence of single trials

Sheraz Khan sherrykhan78 at gmail.com
Tue Nov 27 13:56:05 CET 2012

```Dear Monika,

As Jan-Mathijs correctly mention Coherence is measure across trials, for
single trial coherence value is one, the method I mention above also can
not escape from this mathematical truth, the associated bias with the
method is almost 0.9.

Sheraz

On Tue, Nov 27, 2012 at 6:49 AM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

> Dear Monika,
>
> It may have escaped your attention while digging to the previous posts,
> but the question has been raised (and answered ;-) ) before. Just for the
> very very last time I will make the following statement:
>
> *Single trial coherence estimates cannot be computed!*
> *
> *
> Perhaps the font size and color will make it memorable ;-). This is due to
> the simple fact that coherence is defined across observations. If you have
> just a single observation, due to the mathematics involved, the coherence
> value will be 1.
> Since you want to do group analysis, I think you really should compute the
> coherence per condition, where each condition should consist of a
> sufficient number of trials. Assuming that the time domain data is
> organised such that you have all trials (irrespective of the condition) in
> a single structure, do something like this.
>
> for each subject
>   cfg = [];
>   cfg.output = 'fourier';
>   cfg.method = 'mtmfft'/'mtmconvol'
>   cfg.keeptrials = 'yes';
>   ...
>   freq = ft_freqanalysis(cfg, data);
>
>   cfg = [];
>   cfg.channelcmb = {something here}
>   cfg.trials = [indices of trials belonging to condition 1];
>   coh1 = ft_connectivityanalysis(cfg, freq); % compute coherence across
> the trials for condition 1
>   cfg.trials = [indices of trials belonging to condition 2];
>   coh2 = ft_connectivityanalysis(cfg, freq); % compute coherence across
> the trials for condition 2
> end
>
>
> Good luck,
>
> Jan-Mathijs
>
>
> On Nov 27, 2012, at 12:25 PM, Monika Mellem wrote:
>
> Thank you Sheraz and Jan-Mathijs for your help!
> Sheraz, if you do have the code to keep single-trial coherence estimates,
> I would much appreciate it if you could pass it along (
> monikamellem at gmail.com).
> And Jan-Mathijs, okay, the necessary statistics make sense, and I will
> z-transform the data too.  But as far as you know, is there no
> implementation already in Fieldtrip to keep the single-trial coherence
> estimates?  I assumed setting cfg.keeptrials = 'yes' would do this, but is
> there something else I'm missing as this doesn't seem to work?  I would
> prefer to try what Fieldtrip has implemented first before integrating
> Sheraz's code into my version of Fieldtrip.
>
> Thank you very much!
> Monika
>
>
> On Tue, Nov 27, 2012 at 3:14 AM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Monika,
>>
>> If you want to test across subjects in  a paired fashion, you can use
>> depsamplesT. Your dependent variable then should contain for each subject
>> and condition the coherence (which of course should be estimated across all
>> trials belonging to that condition). Even better would be to perform a
>> so-called Z-transformation to the data. For some inspiration you could have
>> a look at the following paper:
>> http://www.jneurosci.org/content/31/18/6750.long
>>
>> Best,
>>
>> Jan-Mathijs
>>
>> On Nov 27, 2012, at 12:22 AM, Monika Mellem wrote:
>>
>> Dear Fieldtrippers,
>>
>> I am trying to calculate coherence estimates on individual trials of our
>> EEG data and then want to perform a within-subjects statistical test, but
>> so far I have not been able to figure out how to do this.  I am able to
>> calculate coherence for our 22 subjects and then perform statistics on the
>> grand average, so I understand the basic usage of these functions
>> (ft_freqanalysis, ft_connectivityanalysis, ft_freqgrandaverage,
>> ft_freqstatistics).  But now we want to do statistical testing on
>> individual subjects.  Is it possible to keep coherence for individual
>> trials in Fieldtrip as they seem necessary for this statistical analysis?
>>
>> I am setting cfg.keeptrials = 'yes' as an input to ft_freqanalysis, and
>> get the cross-spectra of individual trials (I also tried computing the
>> fourier spectra but it made no difference in the following step).  However,
>> when computing the coherence in ft_connectivityanalysis, Fieldtrip averages
>> over the trials.  Is there a way to output coherence for individual trials
>>
>> Also, I did look into the option of cfg.statistic = 'indepsamplesZcoh' as
>> an input to ft_freqstatistics since previous posts suggested this was for
>> single subject coherence statistics, but our data is paired as the same
>> stimulus appears in the 2 conditions we are comparing.  Is there a paired
>> test for single subject coherence testing, or should we use cfg.statistic =
>> 'depsamplesT'?
>>
>> Many thanks for any suggestions you may have!
>> Monika
>> ________________
>> Monika Mellem
>> PhD Candidate
>> Interdisciplinary Program in Neuroscience
>> Georgetown University
>> Washington, DC
>> msm79 at georgetown.edu
>> 202-687-2687
>>
>> ***********************************************************************
>> cfg settings for ft_freqanalysis and ft_connectivityanalysis
>> ***********************************************************************
>> cfg = [];
>> cfg.prestim = -0.5;
>> cfg.poststim = 1.5;
>> cfg.foilim = [2 30];
>> cfg.freqrange = 'low';
>> % cfg.output     = 'fourier';
>> cfg.output     = 'powandcsd';
>> cfg.method = 'mtmconvol';
>> cfg.keeptrials = 'yes';
>> cfg.channel    = {'all'};
>> cfg.channelcmb = {refchan 'all'};
>>
>> cfgcoh=[];
>> cfgcoh.channelcmb = cfg.channelcmb;
>> cfgcoh.method = 'coh';
>>
>> v = genvarname(['CRSP_' condition '_low']);
>> eval([v '= ft_multitaper_powcoh_EGI(cfg, data);']);  %Wrapper around
>> ft_freqanalysis
>>
>> w = genvarname(['COH_' condition '_low']);
>> eval([w '= ft_connectivityanalysis(cfgcoh, ' v ');']);
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>    Jan-Mathijs Schoffelen, MD PhD
>>
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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